Mon 24 Dec 07:27:37 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2op5-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2op5-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2op5-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:27:42 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 521 and 0 Target number of residues in the AU: 521 Target solvent content: 0.5936 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-3.2-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.70 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 73.087 3.200 Wilson plot Bfac: 49.79 12025 reflections ( 99.86 % complete ) and 0 restraints for refining 6264 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3333 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2831 (Rfree = 0.000) for 6264 atoms. Found 37 (56 requested) and removed 85 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.96 3.16 Search for helices and strands: 0 residues in 0 chains, 6357 seeds are put forward NCS extension: 0 residues added, 6357 seeds are put forward Round 1: 275 peptides, 54 chains. Longest chain 12 peptides. Score 0.323 Round 2: 336 peptides, 57 chains. Longest chain 15 peptides. Score 0.435 Round 3: 365 peptides, 55 chains. Longest chain 17 peptides. Score 0.514 Round 4: 356 peptides, 56 chains. Longest chain 15 peptides. Score 0.487 Round 5: 357 peptides, 53 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 5 Chains 53, Residues 304, Estimated correctness of the model 16.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11719 restraints for refining 5125 atoms. 10556 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2516 (Rfree = 0.000) for 5125 atoms. Found 31 (46 requested) and removed 36 (23 requested) atoms. Cycle 2: After refmac, R = 0.2383 (Rfree = 0.000) for 5089 atoms. Found 15 (45 requested) and removed 32 (22 requested) atoms. Cycle 3: After refmac, R = 0.2342 (Rfree = 0.000) for 5058 atoms. Found 13 (45 requested) and removed 25 (22 requested) atoms. Cycle 4: After refmac, R = 0.2281 (Rfree = 0.000) for 5042 atoms. Found 10 (45 requested) and removed 24 (22 requested) atoms. Cycle 5: After refmac, R = 0.2217 (Rfree = 0.000) for 5025 atoms. Found 9 (45 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 3.21 Search for helices and strands: 0 residues in 0 chains, 5199 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5214 seeds are put forward Round 1: 317 peptides, 57 chains. Longest chain 15 peptides. Score 0.393 Round 2: 350 peptides, 54 chains. Longest chain 15 peptides. Score 0.493 Round 3: 363 peptides, 56 chains. Longest chain 17 peptides. Score 0.501 Round 4: 353 peptides, 55 chains. Longest chain 15 peptides. Score 0.490 Round 5: 377 peptides, 49 chains. Longest chain 17 peptides. Score 0.586 Taking the results from Round 5 Chains 49, Residues 328, Estimated correctness of the model 37.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11580 restraints for refining 5127 atoms. 10317 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2450 (Rfree = 0.000) for 5127 atoms. Found 29 (46 requested) and removed 37 (23 requested) atoms. Cycle 7: After refmac, R = 0.2416 (Rfree = 0.000) for 5097 atoms. Found 15 (45 requested) and removed 36 (22 requested) atoms. Cycle 8: After refmac, R = 0.2327 (Rfree = 0.000) for 5068 atoms. Found 11 (45 requested) and removed 31 (22 requested) atoms. Cycle 9: After refmac, R = 0.2245 (Rfree = 0.000) for 5045 atoms. Found 3 (45 requested) and removed 25 (22 requested) atoms. Cycle 10: After refmac, R = 0.2195 (Rfree = 0.000) for 5021 atoms. Found 10 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.98 3.19 Search for helices and strands: 0 residues in 0 chains, 5191 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5205 seeds are put forward Round 1: 311 peptides, 55 chains. Longest chain 15 peptides. Score 0.399 Round 2: 354 peptides, 53 chains. Longest chain 18 peptides. Score 0.509 Round 3: 344 peptides, 49 chains. Longest chain 21 peptides. Score 0.525 Round 4: 350 peptides, 52 chains. Longest chain 16 peptides. Score 0.510 Round 5: 341 peptides, 47 chains. Longest chain 19 peptides. Score 0.536 Taking the results from Round 5 Chains 48, Residues 294, Estimated correctness of the model 22.7 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11613 restraints for refining 5127 atoms. 10414 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2412 (Rfree = 0.000) for 5127 atoms. Found 28 (46 requested) and removed 34 (23 requested) atoms. Cycle 12: After refmac, R = 0.2391 (Rfree = 0.000) for 5103 atoms. Found 23 (45 requested) and removed 27 (22 requested) atoms. Cycle 13: After refmac, R = 0.2343 (Rfree = 0.000) for 5087 atoms. Found 17 (45 requested) and removed 27 (22 requested) atoms. Cycle 14: After refmac, R = 0.2345 (Rfree = 0.000) for 5074 atoms. Found 17 (45 requested) and removed 26 (22 requested) atoms. Cycle 15: After refmac, R = 0.2274 (Rfree = 0.000) for 5059 atoms. Found 10 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.96 3.16 Search for helices and strands: 0 residues in 0 chains, 5227 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 5251 seeds are put forward Round 1: 277 peptides, 50 chains. Longest chain 16 peptides. Score 0.369 Round 2: 322 peptides, 49 chains. Longest chain 17 peptides. Score 0.480 Round 3: 325 peptides, 48 chains. Longest chain 14 peptides. Score 0.495 Round 4: 335 peptides, 51 chains. Longest chain 18 peptides. Score 0.489 Round 5: 337 peptides, 49 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 5 Chains 49, Residues 288, Estimated correctness of the model 14.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11832 restraints for refining 5127 atoms. 10729 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2431 (Rfree = 0.000) for 5127 atoms. Found 26 (46 requested) and removed 29 (23 requested) atoms. Cycle 17: After refmac, R = 0.2365 (Rfree = 0.000) for 5117 atoms. Found 16 (45 requested) and removed 28 (22 requested) atoms. Cycle 18: After refmac, R = 0.2284 (Rfree = 0.000) for 5101 atoms. Found 20 (45 requested) and removed 24 (22 requested) atoms. Cycle 19: After refmac, R = 0.2237 (Rfree = 0.000) for 5093 atoms. Found 19 (45 requested) and removed 23 (22 requested) atoms. Cycle 20: After refmac, R = 0.2176 (Rfree = 0.000) for 5085 atoms. Found 11 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 3.20 Search for helices and strands: 0 residues in 0 chains, 5223 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 5241 seeds are put forward Round 1: 281 peptides, 49 chains. Longest chain 16 peptides. Score 0.389 Round 2: 324 peptides, 51 chains. Longest chain 18 peptides. Score 0.466 Round 3: 325 peptides, 51 chains. Longest chain 25 peptides. Score 0.468 Round 4: 312 peptides, 44 chains. Longest chain 18 peptides. Score 0.505 Round 5: 320 peptides, 50 chains. Longest chain 24 peptides. Score 0.466 Taking the results from Round 4 Chains 44, Residues 268, Estimated correctness of the model 12.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11786 restraints for refining 5127 atoms. 10758 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2354 (Rfree = 0.000) for 5127 atoms. Found 32 (46 requested) and removed 24 (23 requested) atoms. Cycle 22: After refmac, R = 0.2330 (Rfree = 0.000) for 5128 atoms. Found 14 (46 requested) and removed 26 (23 requested) atoms. Cycle 23: After refmac, R = 0.2320 (Rfree = 0.000) for 5111 atoms. Found 11 (45 requested) and removed 22 (22 requested) atoms. Cycle 24: After refmac, R = 0.2291 (Rfree = 0.000) for 5096 atoms. Found 14 (45 requested) and removed 22 (22 requested) atoms. Cycle 25: After refmac, R = 0.2272 (Rfree = 0.000) for 5085 atoms. Found 18 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 3.20 Search for helices and strands: 0 residues in 0 chains, 5234 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5248 seeds are put forward Round 1: 317 peptides, 58 chains. Longest chain 18 peptides. Score 0.383 Round 2: 333 peptides, 55 chains. Longest chain 18 peptides. Score 0.448 Round 3: 325 peptides, 50 chains. Longest chain 19 peptides. Score 0.477 Round 4: 327 peptides, 51 chains. Longest chain 19 peptides. Score 0.472 Round 5: 330 peptides, 49 chains. Longest chain 18 peptides. Score 0.496 Taking the results from Round 5 Chains 49, Residues 281, Estimated correctness of the model 10.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11965 restraints for refining 5127 atoms. 10890 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2260 (Rfree = 0.000) for 5127 atoms. Found 29 (46 requested) and removed 26 (23 requested) atoms. Cycle 27: After refmac, R = 0.2177 (Rfree = 0.000) for 5122 atoms. Found 18 (46 requested) and removed 23 (23 requested) atoms. Cycle 28: After refmac, R = 0.2119 (Rfree = 0.000) for 5113 atoms. Found 15 (45 requested) and removed 22 (22 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2071 (Rfree = 0.000) for 5103 atoms. Found 14 (45 requested) and removed 22 (22 requested) atoms. Cycle 30: After refmac, R = 0.2028 (Rfree = 0.000) for 5092 atoms. Found 6 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.02 3.23 Search for helices and strands: 0 residues in 0 chains, 5254 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5274 seeds are put forward Round 1: 291 peptides, 52 chains. Longest chain 17 peptides. Score 0.382 Round 2: 314 peptides, 47 chains. Longest chain 17 peptides. Score 0.482 Round 3: 321 peptides, 50 chains. Longest chain 14 peptides. Score 0.468 Round 4: 303 peptides, 45 chains. Longest chain 14 peptides. Score 0.477 Round 5: 312 peptides, 51 chains. Longest chain 14 peptides. Score 0.440 Taking the results from Round 2 Chains 47, Residues 267, Estimated correctness of the model 5.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 12022 restraints for refining 5126 atoms. 11001 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2093 (Rfree = 0.000) for 5126 atoms. Found 16 (46 requested) and removed 23 (23 requested) atoms. Cycle 32: After refmac, R = 0.2033 (Rfree = 0.000) for 5110 atoms. Found 12 (45 requested) and removed 22 (22 requested) atoms. Cycle 33: After refmac, R = 0.2025 (Rfree = 0.000) for 5096 atoms. Found 21 (45 requested) and removed 23 (22 requested) atoms. Cycle 34: After refmac, R = 0.1985 (Rfree = 0.000) for 5094 atoms. Found 10 (45 requested) and removed 23 (22 requested) atoms. Cycle 35: After refmac, R = 0.1922 (Rfree = 0.000) for 5080 atoms. Found 6 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.01 3.22 Search for helices and strands: 0 residues in 0 chains, 5191 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 5216 seeds are put forward Round 1: 261 peptides, 52 chains. Longest chain 13 peptides. Score 0.309 Round 2: 275 peptides, 43 chains. Longest chain 18 peptides. Score 0.435 Round 3: 307 peptides, 52 chains. Longest chain 15 peptides. Score 0.419 Round 4: 291 peptides, 48 chains. Longest chain 18 peptides. Score 0.422 Round 5: 301 peptides, 48 chains. Longest chain 13 peptides. Score 0.444 Taking the results from Round 5 Chains 48, Residues 253, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 12063 restraints for refining 5127 atoms. 11099 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2151 (Rfree = 0.000) for 5127 atoms. Found 21 (46 requested) and removed 25 (23 requested) atoms. Cycle 37: After refmac, R = 0.2048 (Rfree = 0.000) for 5118 atoms. Found 14 (45 requested) and removed 22 (22 requested) atoms. Cycle 38: After refmac, R = 0.2066 (Rfree = 0.000) for 5110 atoms. Found 6 (45 requested) and removed 22 (22 requested) atoms. Cycle 39: After refmac, R = 0.2038 (Rfree = 0.000) for 5090 atoms. Found 8 (45 requested) and removed 23 (22 requested) atoms. Cycle 40: After refmac, R = 0.2021 (Rfree = 0.000) for 5073 atoms. Found 16 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.00 3.21 Search for helices and strands: 0 residues in 0 chains, 5202 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5216 seeds are put forward Round 1: 259 peptides, 49 chains. Longest chain 13 peptides. Score 0.336 Round 2: 256 peptides, 41 chains. Longest chain 17 peptides. Score 0.412 Round 3: 277 peptides, 45 chains. Longest chain 15 peptides. Score 0.420 Round 4: 272 peptides, 41 chains. Longest chain 23 peptides. Score 0.448 Round 5: 288 peptides, 44 chains. Longest chain 18 peptides. Score 0.454 Taking the results from Round 5 Chains 44, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 12070 restraints for refining 5127 atoms. 11138 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2112 (Rfree = 0.000) for 5127 atoms. Found 26 (46 requested) and removed 24 (23 requested) atoms. Cycle 42: After refmac, R = 0.2056 (Rfree = 0.000) for 5125 atoms. Found 20 (46 requested) and removed 23 (23 requested) atoms. Cycle 43: After refmac, R = 0.1984 (Rfree = 0.000) for 5120 atoms. Found 10 (45 requested) and removed 22 (22 requested) atoms. Cycle 44: After refmac, R = 0.1960 (Rfree = 0.000) for 5104 atoms. Found 13 (45 requested) and removed 23 (22 requested) atoms. Cycle 45: After refmac, R = 0.1914 (Rfree = 0.000) for 5091 atoms. Found 11 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 3.21 Search for helices and strands: 0 residues in 0 chains, 5188 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 5218 seeds are put forward Round 1: 245 peptides, 47 chains. Longest chain 16 peptides. Score 0.322 Round 2: 272 peptides, 44 chains. Longest chain 14 peptides. Score 0.418 Round 3: 301 peptides, 48 chains. Longest chain 17 peptides. Score 0.444 Round 4: 313 peptides, 46 chains. Longest chain 16 peptides. Score 0.489 Round 5: 298 peptides, 43 chains. Longest chain 17 peptides. Score 0.485 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 46, Residues 267, Estimated correctness of the model 7.7 % 2 chains (18 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2op5-3_warpNtrace.pdb as input Building loops using Loopy2018 46 chains (267 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12025 reflections ( 99.86 % complete ) and 11665 restraints for refining 5127 atoms. 10565 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2080 (Rfree = 0.000) for 5127 atoms. Found 0 (46 requested) and removed 19 (23 requested) atoms. Cycle 47: After refmac, R = 0.2027 (Rfree = 0.000) for 5102 atoms. Found 0 (45 requested) and removed 12 (22 requested) atoms. Cycle 48: After refmac, R = 0.1985 (Rfree = 0.000) for 5087 atoms. Found 0 (45 requested) and removed 6 (22 requested) atoms. Cycle 49: After refmac, R = 0.1956 (Rfree = 0.000) for 5079 atoms. TimeTaking 52.63